4ACY
Selenomethionine derivative of the GH99 endo-alpha-mannosidase from Bacteroides thetaiotaomicron
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 5.5 | 0.25 M NH4CL, 20% W/V PEG 3350, 0.1 M MES PH 6.5, 5 MM TCEP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.4 | 49.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 47.721 | α = 103.45 |
b = 60.002 | β = 102.59 |
c = 78.666 | γ = 98.59 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | CCD | MARRESEARCH | MIRRORS | 2009-10-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.7 | 50 | 95.8 | 0.06 | 14.4 | 3.7 | 81218 | 2 | 19.2 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.7 | 1.76 | 91.8 | 0.48 | 4.9 | 3.5 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | SAD | THROUGHOUT | NONE | 1.69 | 73.82 | 81218 | 4267 | 93.59 | 0.17676 | 0.17516 | 0.20756 | RANDOM | 21.241 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
1.09 | -1.09 | 0.55 | -0.28 | -0.42 | -1.1 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.237 |
r_dihedral_angle_4_deg | 15.481 |
r_dihedral_angle_3_deg | 12.289 |
r_dihedral_angle_1_deg | 5.876 |
r_angle_refined_deg | 1.23 |
r_nbtor_refined | 0.313 |
r_nbd_refined | 0.203 |
r_symmetry_vdw_refined | 0.198 |
r_symmetry_hbond_refined | 0.154 |
r_xyhbond_nbd_refined | 0.105 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5410 |
Nucleic Acid Atoms | |
Solvent Atoms | 652 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
SHELX | phasing |
ARP/wARP | phasing |
REFMAC | refinement |